Sorry I'm so late in replying, just saw your post.
We will not be paddling in HIGH risk malaria zones. It is definitely a personal choice, but none of us guides take malaria meds. I'd say about 50% of the people who come with us do, and 50% don't. We are super careful about not being on the river past dusk, we always have a shuttle driver waiting for us, and we know where we are going. So, in theory, we shouldn't ever be standing around the jungle acting like mosquito bait!
Typhoid is a good idea, and it's fairly cheap.
I would also recommend Yellow Fever. Again, we are not in a high risk area, but that is just something that is not worth messing with since, to date, they have no cure for it.
Everyone living in the US probably/should have Hep. A and B already, so you should be set there.
The only bugs that I consider somewhat of a problem in Ecuador are the annoying little ankle biter bugs. They are NOT dangerous, just annoying. BUT, you can easily avoid being bitten by wearing pants while boating. Anything will do: thin capeline pants, light weight nylon pants, or even just tall socks (they are ankle biters after all).
I hope this helps.
The water levels have been awesome down here, and we've had week upon week of excellent paddling. If you need anything to help you get excited about your trip, check out Small World Adventures--Kayak Ecuador
See you soon.